Neuropeptide tyrosine (NPY) is a potent orexigenic neuropeptide implicated in feeding regulation in rodents. However, the involvement of NPY in feeding behavior has not well been studied in fish. Therefore, we investigated the role of NPY in food intake using a tiger puffer (Takifugu rubripes) model. We observed the distribution of NPY-like immunoreactivity in the brain. Neuronal cell bodies containing NPY were located in the telencephalon, hypothalamus, mesencephalon, and medulla oblongata, and their nerve fibers were also found throughout the brain. We cloned two cDNAs, encoding NPYa and NPYb orthologs, respectively, from the brain, and also confirmed two genes encoding these NPYs in the Takifugu genome database. We examined the distribution of these transcripts in the brain using real-time PCR. Levels of NPYa mRNA in the telencephalon, mesencephalon and hypothalamus were much higher than in the medulla oblongata and cerebellum, whereas levels of NPYb mRNA in the medulla oblongata were higher than in other regions. We also examined prandial effects on the expression level of these transcripts in the telencephalon and hypothalamus. NPYa mRNA levels in the hypothalamus, but not in the telencephalon, obtained from fish fasted for one week were higher than those in fish that had been fed normally. The level was decreased at 2 h after feeding. Levels of NPYb mRNA were not affected by prandial conditions. These results suggest that NPY is present throughout the brain, and that NPYa, but not NPYb, in the hypothalamus is involved in the feeding regulation in the tiger puffer.